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SPCS1 signal peptidase complex subunit 1 [ Homo sapiens (human) ]

Gene ID: 28972, updated on 5-Mar-2024

Summary

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Official Symbol
SPCS1provided by HGNC
Official Full Name
signal peptidase complex subunit 1provided by HGNC
Primary source
HGNC:HGNC:23401
See related
Ensembl:ENSG00000114902 MIM:610358; AllianceGenome:HGNC:23401
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
SPC1; SPC12; HSPC033; YJR010C-A
Summary
Predicted to enable peptidase activity and ribosome binding activity. Involved in viral protein processing and virion assembly. Is integral component of endoplasmic reticulum membrane. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in kidney (RPKM 60.9), colon (RPKM 57.9) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
3p21.1
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (52706106..52711148)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (52739017..52744058)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (52740122..52745164)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene G protein nucleolar 3 Neighboring gene small nucleolar RNA, C/D box 69 Neighboring gene glycosyltransferase 8 domain containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14451 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19946 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14452 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:52749367-52749954 Neighboring gene NIMA related kinase 4 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:52765581-52766780 Neighboring gene zinc finger protein 610 pseudogene Neighboring gene AK3 pseudogene 7

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. SPCS1-Dependent E2-p7 processing determines HCV Assembly efficiency. Alzahrani N, et al. PLoS Pathog, 2022 Feb. PMID 35130329, Free PMC Article
  2. Allelic expression analysis of the osteoarthritis susceptibility locus that maps to chromosome 3p21 reveals cis-acting eQTLs at GNL3 and SPCS1. Gee F, et al. BMC Med Genet, 2014 May 4. PMID 24886551, Free PMC Article
  3. Host Factor SPCS1 Regulates the Replication of Japanese Encephalitis Virus through Interactions with Transmembrane Domains of NS2B. Ma L, et al. J Virol, 2018 Jun 15. PMID 29593046, Free PMC Article
  4. Signal peptidase complex subunit 1 participates in the assembly of hepatitis C virus through an interaction with E2 and NS2. Suzuki R, et al. PLoS Pathog, 2013. PMID 24009510, Free PMC Article
  5. Structure of the human signal peptidase complex reveals the determinants for signal peptide cleavage. Liaci AM, et al. Mol Cell, 2021 Oct 7. PMID 34388369

See all (37) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. SPCS1-Dependent E2-p7 processing determines HCV Assembly efficiency.
    Title: SPCS1-Dependent E2-p7 processing determines HCV Assembly efficiency.
  2. the results demonstrate that SPCS1 affects viral replication by interacting with NS2B, thereby influencing the posttranslational processing of Japanese Encephalitis Virus proteins and the assembly of virions.
    Title: Host Factor SPCS1 Regulates the Replication of Japanese Encephalitis Virus through Interactions with Transmembrane Domains of NS2B.
  3. cis-acting regulatory polymorphisms acting on GNL3 and SPCS1 contribute to the OA association signal at chromosome 3p21, and these genes therefore merit further investigation.
    Title: Allelic expression analysis of the osteoarthritis susceptibility locus that maps to chromosome 3p21 reveals cis-acting eQTLs at GNL3 and SPCS1.
  4. SPCS1 plays a key role in the formation of the membrane-associated NS2-E2 complex via its interaction with NS2 and E2, which leads to a coordinating interaction between the structural and non-structural proteins
    Title: Signal peptidase complex subunit 1 participates in the assembly of hepatitis C virus through an interaction with E2 and NS2.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Biological insights from 108 schizophrenia-associated genetic loci.
EBI GWAS Catalog
Genome-wide association analysis identifies 13 new risk loci for schizophrenia.
EBI GWAS Catalog
Large-scale genome-wide association analysis of bipolar disorder identifies a new susceptibility locus near ODZ4.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables molecular_function ND
No biological Data available
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in protein targeting to ER IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in proteolysis TAS
Traceable Author Statement
more info
 PubMed 
involved_in signal peptide processing IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in signal peptide processing IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in viral protein processing IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in virion assembly IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in endoplasmic reticulum membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in endoplasmic reticulum membrane TAS
Traceable Author Statement
more info
  
part_of signal peptidase complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of signal peptidase complex IPI
Inferred from Physical Interaction
more info
 PubMed 
part_of signal peptidase complex TAS
Traceable Author Statement
more info
 PubMed 

General protein information

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Preferred Names
signal peptidase complex subunit 1
Names
SPase 12 kDa subunit
microsomal signal peptidase 12 kDa subunit
signal peptidase 12kDa
signal peptidase complex 12 kDa subunit
signal peptidase complex subunit 1 homolog
NP_054760.4

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_014041.5 → NP_054760.4  signal peptidase complex subunit 1

    Status: VALIDATED

    Source sequence(s)
    AC104446, AK027426, BC000884, CA309210, DB459917
    Consensus CDS
    CCDS33769.3
    UniProtKB/TrEMBL
    A0A5F9YFS9
    Related
    ENSP00000478310.2, ENST00000619898.5
    Conserved Domains (1) summary
    pfam06645
    Location:12 → 81
    SPC12; Microsomal signal peptidase 12 kDa subunit (SPC12)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    52706106..52711148
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    52739017..52744058
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9Y6A9.5 GenPept UniProtKB/Swiss-Prot:Q9Y6A9

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Chemical Information
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